bkgdCorrect {codelink}R Documentation

Background correction of intensity values.

Description

Takes a Codelink object with Spot mean and Bkgd median values and corrects applying one of the methods available.

Usage

  bkgdCorrect(object, method="half", preserve=FALSE,
              verbose=TRUE, offset=0)

Arguments

object character; an object of class "Codelink".
method character; the correction method to use, one of "none", "subtract", "half" and "normexp".
preserve logical; if Smean and Bmedian slots should be preserved.
verbose logical; if TRUE print some information with method normexp.
offset numeric; value to add to intensities.

Details

Available methods are: . None: Left intensities untouched. . Subtract: Simple subtraction of Bkgd median from Spot mean. . Half: The same as above but aboid negative values setting all intensity values below zero to 0.5. . Normexp: Apply normexp background adjustment from package limma.

Value

An object of class Codelink with corrected intensity values, that is Ri slot.

Note

Author(s)

Diego Diez

See Also

Examples

#    data(codelink.example)
#    codelink.example <- bkgdCorrect(codelink.example, method="half")

[Package codelink version 1.4.0 Index]